/*
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 *    Copy.java
 *    Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.filters.unsupervised.attribute;

import java.util.Enumeration;
import java.util.Vector;

import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.SparseInstance;
import weka.core.Utils;
import weka.core.WeightedAttributesHandler;
import weka.core.WeightedInstancesHandler;
import weka.filters.Filter;
import weka.filters.StreamableFilter;
import weka.filters.UnsupervisedFilter;

/**
 * <!-- globalinfo-start --> An instance filter that copies a range of
 * attributes in the dataset. This is used in conjunction with other filters
 * that overwrite attribute values during the course of their operation -- this
 * filter allows the original attributes to be kept as well as the new
 * attributes.
 * <p/>
 * <!-- globalinfo-end -->
 * 
 * <!-- options-start --> Valid options are:
 * <p/>
 * 
 * <pre>
 * -R &lt;index1,index2-index4,...&gt;
 *  Specify list of columns to copy. First and last are valid
 *  indexes. (default none)
 * </pre>
 * 
 * <pre>
 * -V
 *  Invert matching sense (i.e. copy all non-specified columns)
 * </pre>
 * 
 * <!-- options-end -->
 * 
 * @author Len Trigg (trigg@cs.waikato.ac.nz)
 * @version $Revision$
 */
public class Copy extends Filter implements UnsupervisedFilter, StreamableFilter, OptionHandler, WeightedInstancesHandler, WeightedAttributesHandler {

    /** for serialization */
    static final long serialVersionUID = -8543707493627441566L;

    /** Stores which columns to copy */
    protected Range m_CopyCols = new Range();

    /**
     * Stores the indexes of the selected attributes in order, once the dataset is
     * seen
     */
    protected int[] m_SelectedAttributes;

    /**
     * Returns an enumeration describing the available options.
     * 
     * @return an enumeration of all the available options.
     */
    @Override
    public Enumeration<Option> listOptions() {

        Vector<Option> newVector = new Vector<Option>(2);

        newVector.addElement(new Option("\tSpecify list of columns to copy. First and last are valid\n" + "\tindexes. (default none)", "R", 1, "-R <index1,index2-index4,...>"));
        newVector.addElement(new Option("\tInvert matching sense (i.e. copy all non-specified columns)", "V", 0, "-V"));

        return newVector.elements();
    }

    /**
     * Parses a given list of options.
     * <p/>
     * 
     * <!-- options-start --> Valid options are:
     * <p/>
     * 
     * <pre>
     * -R &lt;index1,index2-index4,...&gt;
     *  Specify list of columns to copy. First and last are valid
     *  indexes. (default none)
     * </pre>
     * 
     * <pre>
     * -V
     *  Invert matching sense (i.e. copy all non-specified columns)
     * </pre>
     * 
     * <!-- options-end -->
     * 
     * @param options the list of options as an array of strings
     * @throws Exception if an option is not supported
     */
    @Override
    public void setOptions(String[] options) throws Exception {

        String copyList = Utils.getOption('R', options);
        if (copyList.length() != 0) {
            setAttributeIndices(copyList);
        }
        setInvertSelection(Utils.getFlag('V', options));

        if (getInputFormat() != null) {
            setInputFormat(getInputFormat());
        }
    }

    /**
     * Gets the current settings of the filter.
     * 
     * @return an array of strings suitable for passing to setOptions
     */
    @Override
    public String[] getOptions() {

        Vector<String> options = new Vector<String>();

        if (getInvertSelection()) {
            options.add("-V");
        }
        if (!getAttributeIndices().equals("")) {
            options.add("-R");
            options.add(getAttributeIndices());
        }

        return options.toArray(new String[0]);
    }

    /**
     * Returns the Capabilities of this filter.
     * 
     * @return the capabilities of this object
     * @see Capabilities
     */
    @Override
    public Capabilities getCapabilities() {
        Capabilities result = super.getCapabilities();
        result.disableAll();

        // attributes
        result.enableAllAttributes();
        result.enable(Capability.MISSING_VALUES);

        // class
        result.enableAllClasses();
        result.enable(Capability.MISSING_CLASS_VALUES);
        result.enable(Capability.NO_CLASS);

        return result;
    }

    /**
     * Sets the format of the input instances.
     * 
     * @param instanceInfo an Instances object containing the input instance
     *                     structure (any instances contained in the object are
     *                     ignored - only the structure is required).
     * @return true if the outputFormat may be collected immediately
     * @throws Exception if a problem occurs setting the input format
     */
    @Override
    public boolean setInputFormat(Instances instanceInfo) throws Exception {

        super.setInputFormat(instanceInfo);

        m_CopyCols.setUpper(instanceInfo.numAttributes() - 1);

        // Create the output buffer
        Instances outputFormat = new Instances(instanceInfo, 0);
        m_SelectedAttributes = m_CopyCols.getSelection();
        for (int current : m_SelectedAttributes) {
            // Create a copy of the attribute with a different name
            Attribute origAttribute = instanceInfo.attribute(current);
            outputFormat.insertAttributeAt(origAttribute.copy("Copy of " + origAttribute.name()), outputFormat.numAttributes());

        }

        // adapt locators
        int[] newIndices = new int[instanceInfo.numAttributes() + m_SelectedAttributes.length];
        for (int i = 0; i < instanceInfo.numAttributes(); i++) {
            newIndices[i] = i;
        }
        for (int i = 0; i < m_SelectedAttributes.length; i++) {
            newIndices[instanceInfo.numAttributes() + i] = m_SelectedAttributes[i];
        }
        initInputLocators(instanceInfo, newIndices);

        setOutputFormat(outputFormat);

        return true;
    }

    /**
     * Input an instance for filtering. Ordinarily the instance is processed and
     * made available for output immediately. Some filters require all instances be
     * read before producing output.
     * 
     * @param instance the input instance
     * @return true if the filtered instance may now be collected with output().
     * @throws IllegalStateException if no input format has been defined.
     */
    @Override
    public boolean input(Instance instance) {

        if (getInputFormat() == null) {
            throw new IllegalStateException("No input instance format defined");
        }
        if (m_NewBatch) {
            resetQueue();
            m_NewBatch = false;
        }

        double[] vals = new double[outputFormatPeek().numAttributes()];
        for (int i = 0; i < getInputFormat().numAttributes(); i++) {
            vals[i] = instance.value(i);
        }
        int j = getInputFormat().numAttributes();
        for (int i = 0; i < m_SelectedAttributes.length; i++) {
            int current = m_SelectedAttributes[i];
            vals[i + j] = instance.value(current);
        }
        Instance inst = null;
        if (instance instanceof SparseInstance) {
            inst = new SparseInstance(instance.weight(), vals);
        } else {
            inst = new DenseInstance(instance.weight(), vals);
        }

        copyValues(inst, false, instance.dataset(), outputFormatPeek());

        push(inst); // No need to copy instance
        return true;
    }

    /**
     * Returns a string describing this filter
     * 
     * @return a description of the filter suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String globalInfo() {

        return "An instance filter that copies a range of attributes in the" + " dataset. This is used in conjunction with other filters that" + " overwrite attribute values during the course of their operation --" + " this filter allows the original attributes to be kept as well" + " as the new attributes.";
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String invertSelectionTipText() {
        return "Sets copy selected vs unselected action." + " If set to false, only the specified attributes will be copied;" + " If set to true, non-specified attributes will be copied.";
    }

    /**
     * Get whether the supplied columns are to be removed or kept
     * 
     * @return true if the supplied columns will be kept
     */
    public boolean getInvertSelection() {

        return m_CopyCols.getInvert();
    }

    /**
     * Set whether selected columns should be removed or kept. If true the selected
     * columns are kept and unselected columns are copied. If false selected columns
     * are copied and unselected columns are kept. <br>
     * Note: use this method before you call <code>setInputFormat(Instances)</code>,
     * since the output format is determined in that method.
     * 
     * @param invert the new invert setting
     */
    public void setInvertSelection(boolean invert) {

        m_CopyCols.setInvert(invert);
    }

    /**
     * Get the current range selection
     * 
     * @return a string containing a comma separated list of ranges
     */
    public String getAttributeIndices() {

        return m_CopyCols.getRanges();
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String attributeIndicesTipText() {
        return "Specify range of attributes to act on." + " This is a comma separated list of attribute indices, with" + " \"first\" and \"last\" valid values. Specify an inclusive" + " range with \"-\". E.g: \"first-3,5,6-10,last\".";
    }

    /**
     * Set which attributes are to be copied (or kept if invert is true)
     * 
     * @param rangeList a string representing the list of attributes. Since the
     *                  string will typically come from a user, attributes are
     *                  indexed from 1. <br>
     *                  eg: first-3,5,6-last<br>
     *                  Note: use this method before you call
     *                  <code>setInputFormat(Instances)</code>, since the output
     *                  format is determined in that method.
     * @throws Exception if an invalid range list is supplied
     */
    public void setAttributeIndices(String rangeList) throws Exception {

        m_CopyCols.setRanges(rangeList);
    }

    /**
     * Set which attributes are to be copied (or kept if invert is true)
     * 
     * @param attributes an array containing indexes of attributes to select. Since
     *                   the array will typically come from a program, attributes
     *                   are indexed from 0.<br>
     *                   Note: use this method before you call
     *                   <code>setInputFormat(Instances)</code>, since the output
     *                   format is determined in that method.
     * @throws Exception if an invalid set of ranges is supplied
     */
    public void setAttributeIndicesArray(int[] attributes) throws Exception {

        setAttributeIndices(Range.indicesToRangeList(attributes));
    }

    /**
     * Main method for testing this class.
     * 
     * @param argv should contain arguments to the filter: use -h for help
     */
    public static void main(String[] argv) {
        runFilter(new Copy(), argv);
    }
}
